In printing devices, accurate registration of marking material drops on passing substrates in the process direction is difficult. This registration is necessary to ensure that the drops from separated heads are printed at the required locations, especially for three-dimensional (3D) printing. Printheads, such as inkjet printheads, fire the appropriate ejectors with reference to a distance signal as print media, a plate, or platform passes the printheads to produce printed media, form 3-D items, or the like. The signal used to coordinate the firing of the ejectors in printheads is generated by an encoder monitoring a roller in the media transport. Unfortunately, the encoder feedback is subject to noise sources including phase-lag between the encoder roller and the print zone where the printheads are located, roller runout, thermal expansion of the encoder roller, and differential thermal expansion of the encoder roller coating. Feed-forward corrections based on measurements taken at a single point in time have been used to compensate for roller runout and thermal expansion. These corrections, however, cannot fully compensate for all of the noise sources. A more robust system of compensating for velocity changes in the print zone would be beneficial.